Now, I understand that in the film the midichlorians were actually meant to BE the Force. I.e. they actually caused Force sensitivity. My understanding is that this IS what Lucas originally meant.
However, just about every other person realized how insane this was and retconned it. I follow the retcon which makes PERFECT SENSE.
Basically, midichlorians are sort of like crayfish. You see, crayfish live only in clean water. They do not cause water to be clean; you couldn't toss a bunch of crayfish into a polluted lake and it would become pristine. They simply only live in clean water, so if you find crayfish in a lake or stream you know the water is clean. They are indicators.
Midichlorians are like crayfish; they are indicators. They show that a particular individual has high Force sensitivity. Oh they grow in every person, but they need high levels of Force sensitivity to really propagate and reach high numbers. So what; Anakin had a level of over 20,000? An average Jedi would probably have something like 5-10 thousand, while a non-Force sensitive would have more like a few hundred or, at most 1,000.
This provides a logical way of determine who was Force sensitive (thus explaining how the Order found new Jedi hopefuls) while still keeping the mysticism of the Force alive. What is it? Well we still don't know, but at least we can kinda measure it indirectly.
I realize this doesn't really answer your question. I don't know what he was thinking, but probably he thought this was a really great idea that the fans would love. The problem is no one challenged him on it so he figured it must be a great idea and stayed with it.
This post, best post.